PUMAdb : Preparing data for publication

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This help document contains guidelines for making microarray data accessible on the web for database users who are ready for submit a manuscript for publication. Please note that it is a strict policy that any data resident in the database that is used in a publication MUST be made publicly accessible within the database.

Appropriate Acknowledgements and Citations

PUMAdb is funded in part by the National Institute of General Medical Sciences (NIGMS) [NIH grant P50 GM071508]. Acknowledgement of this support in your publication is required.

PUMAdb is based on the Stanford Microarray Database package. Therefore, to reference the software package in a paper, you may want to reference:

Gollub J, Ball CA, Binkley G, Demeter J, Finkelstein DB, Hebert JM, Hernandez-Boussard T, Jin H, Kaloper M, Matese JC, Schroeder M, Brown PO, Botstein D, Sherlock G. The Stanford Microarray Database: data access and quality assessment tools. Nucleic Acids Res. 2003 Jan 1;31(1):94-6. PDF  |  PubMed

Or the prior publication:

Sherlock G, Hernandez-Boussard T, Kasarskis A, Binkley G, Matese JC, Dwight SS, Kaloper M, Weng S, Jin H, Ball CA, Eisen MB, Spellman PT, Brown PO, Botstein D, Cherry JM. The Stanford Microarray Database. Nucleic Acids Res 2001 Jan 1;29(1):152-5.
PDF  |  PubMed

If you want to refer to a URL for PUMAdb, please use:

Note: We warn against publishing any url besides the above. Otherwise, we cannot guarantee that your preferred URL url will always work, as software and hardware changes.

Creating a Website

There are a couple of possibilities:

  1. You can make the web-site on your own and you can host it on your own.
  2. You can make the web-site on your own and you can ask us to host it. If you choose this, please let us know well ahead of time by sending e-mail to array@princeton.edu.
  3. Ask PUMAdb ahead of time to help you with making one. Usually, given the amount of work that this entails, the curator who creates the website expects collaborative consideration. Please send an e-mail to Please send an e-mail to array@princeton.edu.

Creating Experiment Sets

The experiments you want to publish need to be combined into an experiment set and the permissions on the set need to be changed, so they would be available publicly. There is help available about how to create experiment sets: Creating Experiment Sets

Permanent Record

Data within the database can change. There are a number of reasons why this could happen, eg. data can be renormalized; the mapping of DNA on the arrays to the genes they represent can be dynamic, as can the annotation of those genes; godlist problems can be found and fixed. While these changes enhance the utility of data stored within the database, they will also make it impossible to repeat an analysis as it was done originally at a later time.

It is the authors responsibility to make sure an analysis can always be repeated and verified in the future. To ensure this, static versions of your raw and processed data - the way it was used in the publication - need to be both:

  1. available on the web-site,
  2. archived on CD in your lab!

Tell the Database Curators

Even if you made your own web-site, we still need to know about the publication. Let us know when the paper is published, so we can associate the reference with your microarray expression data: array@princeton.edu.

To let the curators know about an upcoming publication, you should create the relevant experiment sets, and email array@princeton.edu with the details of those sets, and the details of the in press paper (also let us know if you have an additional web supplement to accompany your paper). Then send us a subsequent email when the paper is actually published, and we will take care of making the data public.

Please note that if you would like to make your data fully available to reveiwers prior to publication, without making it available to the whole world (a reasonable, and indeed good thing), then please send us email. We will then create a reviewer account, and grant it privileges to see the experiment sets that you are using to support the publication.